Sorry for not being more clear. I'm agreeing that the speeds are akin to that of a USB 2.0 rather than a USB 3.0.
Yes, drives do make a great difference as well. I have some slow drives that won't go faster than 60 GB/s regardless of being installed in a USB 3.0 enclosure or connected directly to a drive sled. Your original post wasn't clear. You didn't state which drive you were using with the USB interface and which drive you were using with the SATA interface.
I've purchased USB 3.0 drives that weren't capable of USB 3.0 speeds. I was trying to determine if this was a possible cause. Since you didn't include your particular configuration I had no way of knowing how you tested.
If you were comparing a 2.5" Toshiba or Hitachi drive, to a 3.5" WD or Segate then your results aren't that surprising. I have several 2.5" USB 3.0 drives that only produce USB 2.0 speeds even when removed from the enclosure and connected directly to an SATA connection rather than a USB connection. With these drives, the limiting factor is the drive, not the USB enclosure or the interface card. I have purchased bare FAST drives and installed them into the same enclosure and they achieve normal USB 3.0 speeds. Do you see why I asked the question? I didn't know your configuration.
I have a 3TB barracuda and it's a particularly fast drive in its class, I have a 2TB My Book and it's a lot slower. That said, you should be getting 90-115 GB/s on th WD depending on the testing method, amount of data on the drive, and drive condition.
If I were you, I would connect the USB drive to another computer and retest. If it's just as slow, you know that the drive/enclosure/cable are the limiting factor in the speed. Your USB 3 kit may be faulty. If you get a much faster result, then it's likely the issue is with the USB card and/or driver issue.